It was supposed to be the day when Mark Cavendish wriggled into the Tour de France's famous yellow jersey for the first time. Instead it will be remembered for an Orica GreenEdge team bus wedged under the finish line and a spectacular crash with six kilometres remaining that took out half the peloton.

With the driver trying – and failing – to extricate the bus, before throwing his hands in front of his eyes as if desperately hoping to wish his worries away, Tour organisers frantically switched the finish to the three-kilometre line down the road. Moments later the bus started reversing – and so did the organisers, who switched the finish back to its original spot near Bastia beach. It was a decision that, in the words of Cavendish, led to "carnage".

With the peloton going at more than 40mph, Cavendish's Omega Pharma-Quickstep team-mate Tony Martin appeared to buckle suddenly, and as his bike jumped and skipped and then slipped from under him several riders were sent flying – including Team Sky's Geraint Thomas. Despite Thomas doing a passable impression of Superman he was cleared to race on Sunday after hospital x-rays showed no damage.

Because of the confusion, everyone was given the same finishing time as the winner, the German Marcel Kittel. That, however, was scant consolation for Cavendish, who blamed the organisers for causing the chaos with their late switch. "We were hearing in the radios with 5k to go the finish was in 2k," he said. "Then a kilometre later, it's at the finish. It was carnage. I'm lucky I didn't come down. Some of my team-mates are a lot worse."

Martin, the world time-trial champion, later lost consciousness twice on the team bus and was reported to have widespread abrasions. Even though a brain scan came back clear the chances of him participating in the second stage from Bastia to Ajaccio must be slim.

If he is ruled out it will be an early and brutal blow to Cavendish's hopes of winning the green jersey again: the German is a key part of the Manxman's sprint train as well as the favourite for the two individual time trials.

Alberto Contador, the second favourite for the Tour, suffered injuries to his shoulders and elbow. "It hurts for sure," he said. "But the Tour is the Tour. These things happen." He was grimacing as he spoke. His pain may yet be Chris Froome's gain.

While the favourites for the green jersey – Cavendish, Peter Sagan and André Greipel – were held up or tripped up by the crash, Kittel was putting another stamp on his emerging talent by racing towards his first Tour stage victory.

Britain's David Millar, who at 36 is still chugging away with the Garmin-Sharp team, was a surprise fourth.

A delighted Kittel, who was forced to pull out during the fifth stage of last year's Tour following a stomach bug, said: "It feels like I have gold on my shoulders. I was looking for Cavendish, I was looking for Greipel and they weren't there, so we decided to go for it. It's by far the greatest day of my whole life. I just hope I can sleep."

Cavendish had warned beforehand that the first stage would be "dangerous", but for the first 190 kilometres of the 212km-stage from Porto-Vecchio the pace was fast but safe.

The only crash in the early stages occurred when Froome rolled into a concrete barrier during the 15 minute neutral zone before the official start, forcing him to change his bike. He tweeted: "I got away somewhat unscathed, except for a minor disagreement with a concrete barrier in the neutral zone. Icepacks working their magic."

Froome admitted that the crash had been "quite a warning", and said he was taking nothing for granted in the three weeks ahead.

"It was a reminder that this Tour is about much more than having the form and being here, it's about staying out of trouble too," he said. "But if that's the only pressure I have this Tour I'll take that.

"I didn't see much. I just saw bikes flying around and people crashing all around. I was just concerned they wouldn't give everyone the bunch time so I chased to get back up."

There was enough drama before the first stage began with French riders meeting their minister of sport, Valérie Fourneyron, to protest at the planned naming of everyone in the peloton who took EPO during the 1998 and 1999 Tours.

The riders feel that by releasing the names on 18 July, the day when the peloton goes up the Alpe d'Huez twice, it will take attention away from the Tour's set piece stage.

The minister also appeared to support them, saying. "Cycling has been the victim of a media lynching,. The Tour is not doping. Doping is not the Tour."

However, the decision is out of her hands. The row will rumble on. And if nothing changes expect another small explosion on 18 July.

Meanwhile, the French wing of the riders' association, Cyclistes Professionels Associés, also felt compelled to respond to Lance Armstrong's interview with Le Monde by telling him: "Enough is enough. Today tolerable limits have been reached! We have for many years demonstrated our goodwill towards an anti-doping!"

At the time it seemed like more than enough exclamation marks for one day. But then we witnessed the finale of a unique and painfully dramatic first stage.